diff --git a/lib/eslint/flat-eslint.js b/lib/eslint/flat-eslint.js
index f2d6082eb3c..4ef38611361 100644
--- a/lib/eslint/flat-eslint.js
+++ b/lib/eslint/flat-eslint.js
@@ -714,12 +714,10 @@ class FlatESLint {
                 }
                 const rule = getRuleFromConfig(ruleId, config);
 
-                // ensure the rule exists
-                if (!rule) {
-                    throw new TypeError(`Could not find the rule "${ruleId}".`);
+                // ignore unknown rules
+                if (rule) {
+                    resultRules.set(ruleId, rule);
                 }
-
-                resultRules.set(ruleId, rule);
             }
         }
 
diff --git a/tests/lib/eslint/flat-eslint.js b/tests/lib/eslint/flat-eslint.js
index c3a8240e7b2..9e0ca12458f 100644
--- a/tests/lib/eslint/flat-eslint.js
+++ b/tests/lib/eslint/flat-eslint.js
@@ -4478,6 +4478,42 @@ describe("FlatESLint", () => {
 
             assert.deepStrictEqual(rulesMeta, { "no-var": coreRules.get("no-var").meta });
         });
+
+        it("should return empty object if all messages are related to unknown rules", async () => {
+            const engine = new FlatESLint({
+                overrideConfigFile: true
+            });
+
+            const results = await engine.lintText("// eslint-disable-line foo, bar/baz, bar/baz/qux");
+
+            assert.strictEqual(results[0].messages.length, 3);
+            assert.strictEqual(results[0].messages[0].ruleId, "foo");
+            assert.strictEqual(results[0].messages[1].ruleId, "bar/baz");
+            assert.strictEqual(results[0].messages[2].ruleId, "bar/baz/qux");
+
+            const rulesMeta = engine.getRulesMetaForResults(results);
+
+            assert.strictEqual(Object.keys(rulesMeta).length, 0);
+        });
+
+        it("should return object with meta of known rules if some messages are related to unknown rules", async () => {
+            const engine = new FlatESLint({
+                overrideConfigFile: true,
+                overrideConfig: { rules: { "no-var": "warn" } }
+            });
+
+            const results = await engine.lintText("// eslint-disable-line foo, bar/baz, bar/baz/qux\nvar x;");
+
+            assert.strictEqual(results[0].messages.length, 4);
+            assert.strictEqual(results[0].messages[0].ruleId, "foo");
+            assert.strictEqual(results[0].messages[1].ruleId, "bar/baz");
+            assert.strictEqual(results[0].messages[2].ruleId, "bar/baz/qux");
+            assert.strictEqual(results[0].messages[3].ruleId, "no-var");
+
+            const rulesMeta = engine.getRulesMetaForResults(results);
+
+            assert.deepStrictEqual(rulesMeta, { "no-var": coreRules.get("no-var").meta });
+        });
     });
 
     describe("outputFixes()", () => {